Colin Kaepernick is atop the list of remaining free-agent quarterbacks and that has sparked a fierce debate about whether or not he’s being blackballed. Kyle Shanahan, the new coach of the 49ers, explained why he didn’t want Kaepernick. “Colin has a certain skill-set that you can put a specific offense to it that he can be very successful in,” he said. “The type of offense I wanted to run was somewhat different.” The Niners have not offered contracts to any of their top four QBs of last season. Instead they signed Brian Hoyer and Matt Barkley, who played on a 3-13 Bears team in 2016. The Niners also have the No. 2 pick in the draft.